Hare-raising adventure in genome assembly

The California sea hare, Aplysia californica, is a species of gastropod molluscs found along the coast of California, United States, and northwestern Mexico. These sea slugs possess the largest nerve cells in the entire animal kingdom, making them a valuable model organism to study the neurobiology of learning and memory [1].

In 2003 Leonid L. Moroz (University of Florida) and Eric R. Kandel (Columbia University) initiated the sequencing of the whole genome of A. californica, which was approved as a priority by National Human Genome Research Institute in March 2005. The Broad Institute, using inbred lines of Aplysia (F4) raised by Tom Capo (NIH Aplysia facility) in collaboration with the Moroz lab generated the first draft assembly for the species in 2006, revised in 2009 and 2013 [2, 3]. Together with Leonid Moroz and his team at the University of Florida we are today releasing a chromosome-length assembly for A. californica based on the 2013 draft from the Broad Institute.

Check out whole-genome alignment of the new assembly to the 14 linkage groups of the channeled applesnail Pomacea canaliculata from (Liu et al., GigaScience, 2018), illustrating, for the first time ever, the conservation of chromosome content across 400 million years of gastropod evolution.

Whole-genome alignment of the new Aplysia californica assembly to the 14 linkage groups of Pomacea canaliculata, from (Liu et al., 2018).

No drama piranha

The red-bellied piranha, also known as the red piranha (Pygocentrus nattereri), is a species of piranha native to South America and a popular aquarium fish. Through media influence, the red-bellied piranha has developed a reputation as a ferocious predator, but scientists believe that the animals’ fearsome reputation has been exaggerated [1].

This week we are releasing the chromosome-length assembly for the red-bellied piranha, based on the work by W.C. Warren and M. Schartl [2]. We are grateful to Moody Gardens for the sample used for Hi-C library preparation!

Check out the alignments of the new assembly to the two most closely related fish genome assemblies out there: the Mexican tetra Astyanax mexicanus, from (McGaugh et al. Nat Commun., 2014), and the channel catfish Ictalurus punctatus, from (Liu et al. Nat Commun., 2016). Looks like the content of the chromosomes is largely preserved.

Whole genome alignments of the red-bellied piranha genome assembly to the assemblies of the Mexican tetra (left) and channel catfish (right).

Turning the leaf for the silkworm caterpillar

Today we are releasing the chromosome-length genome assembly for the silkmoth Bombyx mori. The caterpillar stage of the silkmoth, the silkworm, is a valuable source of silk. A single silkworm produces a single continuous silk thread up to 1,300 meters (4,250 feet) in length, and it takes 1700 to 2000 silkworm cocoons to make one silk dress [1]!

The new genome assembly, shared here, is based on the work from the International Silkworm Genome Consortium (International Silkworm Genome Consortium, Insect Biochemistry and Molecular Biology, 2008). The Hi-C data for the upgrade was generated using insects from the Carolina Biological Supply Company.

To validate the assembly, we compare the positions of 1,451 SNP markers from the Silkworm Genome Research Program website predicted from linkage mapping with their coordinates on the new assembly, below. The datasets are in excellent agreement!

Comparison of SNP marker positions according to the linkage data and predicted by the new assembly.